NEWS.md

In Rekyt/funrar: Functional Rarity Indices Computation

funrar 1.5.0

NEW FEATURES

• Added a new vignette named "other_functions" to document recently added functions. You can access it through vignette("other_functions", package = "funrar")

INTERNAL CHANGES

• Fix uses of the Matrix package for their next version
• Reorganized documentation to please goodpractice

USER-FACING CHANGES

• Remove warnings regarding relative abundances for the distinctiveness_*() functions as they can perfectly work with absolute abundances giving the same results.
• Fix typo in name of sparse matrices vignette.

funrar 1.4.1

BUG FIX

• fix use of tidytext for upcoming version (#42, thanks @juliasilge !)
• remove dependency on dplyr to avoid breaking due to next dplyr release

funrar 1.4.0

NEW FEATURES

• Implement distinctiveness_global() to compute occurrence based distinctiveness at the global/regional level using only a distance matrix

BUG FIX

• Fix tests that used data.frame() now with explicit stringAsFactors values for compatibility with R 4.0.0
• Add missing tests on bad inputs for some functions

funrar 1.3.1

BUG FIX

• Test explicitly for matrix type in rarity_dimensions() for compatibility with R 4.0.0

funrar 1.3.0

NEW FEATURES

• Add _tidy() aliases for each _stack() function for easier reading (fix #29).
• distinctiveness_stack() returns NA as distinctiveness values for absent species (#30).
• New definition of functional distinctiveness based on range see distinctiveness_range().
• New definition of functional distinctiveness based on range with different formula see distinctiveness_alt().

BUG FIX

• Warning when distinctiveness equals NaN in distinctiveness_stack() (#30).

funrar 1.2.2

• Fix a bug in the test of distinctiveness_dimensions() that generated errors on cran server.

funrar 1.2.1

• Add Authors' ORCID and all contributors;
• funrar paper is now included in DESCRIPTION, README.md and has a proper CITATION file;
• Fix typos in documentation;
• Transformation from tidy data.frame to sparse matrix is now possible using stack_to_matrix(x, sparse = TRUE) (#25);
• Add a warning message when using only continuous traits with function comput_dist_matrix(), as it defaults to Gower's distance (#27);
• Specification in help that functional distances need to be scaled between 0 and 1 prior to distinctiveness computation (#26).

funrar 1.2.0

• Split rarity_dimensions() in two more explicit functions: uniqueness_dimensions() and distinctiveness_dimensions() split corresponding tests;
• Add internal function to compute multiple functional distance matrix using a single trait table (combination_trait_dist());
• distinctiveness() now fully conserve the dimnames of the provided site-species matrix.

funrar 1.1.1

• Add tests for rarity_dimensions();
• rarity_dimensions() now comprises both Uniqueness and Distinctiveness;
• Remove packages StatMatch, microbenchmark & reshape2 from suggested packages.

funrar 1.1.0

• Made make_absolute() defunct because it was based on false assumptions and would not give back matrices of relative abundances;
• Improved examples of make_relative(), uniqueness(), distinctiveness() to compute across single communities or regional pools;
• Add rarity_dimensions() function to measure the different facets of rarity according to the trait;
• Add center and scale arguments in compute_dist_matrix() to scale traits before computing distance, these arguments are sensitive to the specific distance metric used;
• Use markdown with roxygen2 to generates documentation.

funrar 1.0.3

• Corrected bug so that dense matrices can be transformed to stack data frame using matrix_to_stack() (#19),
• Updated citation for Violle et al. 2017,
• Use package goodpractice to enforce better code style,
• Add is_relative() function to test if matrix contains relative abundances, scarcity() and distinctiveness() now warns if it is not the case (#21),
• Conditional use microbenchmark following CRAN advice.

funrar 1.0.2

• Added functions to convert absolute abundance matrix to relative abundance matrix, make_relative() and reverse function make_absolute(),
• Added a NEWS.md file to track changes to the package.

Rekyt/funrar documentation built on April 12, 2024, 3:24 p.m.